Basalt is an important geotechnical material for engineering construction in Southwest China. However, it has complicated structural features due to its special origin, particularly the widespread occurrence of hidden cracks. Such discontinuities significantly affect the mechanical properties and engineering stability of basalt, and related research is lacking and unsystematic. In this work, taking the underground caverns in the Baihetan Hydropower Station as the engineering background, the size-dependent mechanical behaviors and excavation responses of basalt with hidden cracks were systematically explored based on a synthetic rock mass (SRM) model combining the finite-discrete element method (FDEM) and discrete fracture network (DFN) method. The results showed that: (1) The DFN–FDEM model generated based on the statistical characteristics of the geometric parameters of hidden cracks can consider the real structural characteristics of basalt, whereby the mechanical behaviors found in laboratory tests and at the engineering site could be exactly reproduced. (2) The representative elementary volume (REV) size of basalt blocks containing hidden cracks was 0.5 m, and the mechanical properties obtained at this size were considered equivalent continuum properties. With an increase in the sample dimensions, the mechanical properties reflected in the stress–strain curves changed from elastic–brittle to elastic–plastic or ductile, the strength failure criterion changed from linear to nonlinear, and the failure modes changed from fragmentation failure to local structure-controlled failure and then to splitting failure. (3) The surrounding rock mass near the excavation face of underground caverns typically showed a spalling failure mode, mainly affected by the complex structural characteristics and high in situ stresses, i.e., a tensile fracture mechanism characterized by stress–structure coupling. The research findings not only shed new light on the failure mechanisms and size-dependent mechanical behaviors of hard brittle rocks represented by basalt but also further enrich the basic theory and technical methods for multi-scale analyses in geotechnical engineering, which could provide a reference for the design optimization, construction scheme formulation, and disaster prevention of deep engineering projects.